Hi Bruce, I've attached zipped tiff images of a tkmedit (where you can see dura being included) and an inflated image of the same subject (where the flattening of the gyri is where the included dura is)...
Let me know if you cannot access the files.
Thanks! Martina
On Wed, Aug 24, 2011 at 9:57 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Martina Can you send us one example dataset? Bruce
On Aug 24, 2011, at 10:52 PM, Martina Ly ly.martina@gmail.com wrote:
Hello freesurfers, Dura is being included in the pial surface of the superior section of the
brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)?
I'm also thinking of using another intensity correction software (i.e.
unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs.
Any suggestions would be appreciated!
Best, Martina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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